List of tools

These are the tools that wrapped inside bacannot. Cite the tools whenever you use its output.

Analysis steps	Used software or databases
Genome assembly (if raw reads are given)	Flye and Unicycler
Identification of closest 10 NCBI Refseq genomes and comparison of genomes	RefSeq Masher and Sourmash
Generic annotation and gene prediction	Prokka or Bakta
rRNA prediction	barrnap
Classification within multi-locus sequence types (STs)	mlst
KEGG KO annotation and visualization	KofamScan and KEGGDecoder
Annotation of secondary metabolites	antiSMASH
Methylation annotation	Nanopolish
Annotation of antimicrobial (AMR) genes	AMRFinderPlus, ARGminer, Resfinder and RGI
Annotation of virulence genes	Victors and VFDB
Prophage sequences and genes annotation	PHASTER, Phigaro and PhySpy
Annotation of integrative and conjugative elements	ICEberg
Annotation of bacterial integrons	Integron Finder
Focused detection of insertion sequences	digIS
In silico detection and typing of plasmids	Plasmidfinder, Platon and MOB-typer
Prediction and visualization of genomic islands	IslandPath-DIMOB and gff-toolbox
Custom annotation from formatted FASTA or NCBI protein IDs	BLAST
Merge of annotation results	bedtools
Genome Browser renderization	JBrowse
Circos plot generation	easy_circos
Renderization of automatic reports and shiny app for results interrogation	R Markdown, Shiny and SequenceServer